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Table 6 AA-15-DNA

From: Compression-based classification of biological sequences and structures via the Universal Similarity Metric: experimental assessment

AA-15-DNA

UCD

NCD

CD

 

UPGMA

NJ

UPGMA

NJ

UPGMA

NJ

Gzip

4

5

6

9

6

9

Bzip2

6

5

6

5

6

5

PPMd16

4

3

4

3

4

5

PPMd8

4

5

4

5

4

5

PPMd4

8

9

10

13

8

13

PPMd2

24

23

24

23

24

23

Gencompress

4

3

4

3

4

5

Huffman

22

21

22

21

22

23

Ac fast

24

21

22

21

24

23

Rc fast

24

23

22

21

24

21

Ac med.

18

23

24

21

22

21

Rc med.

24

23

22

19

24

21

Ac slow

24

15

16

15

16

17

Rc slow

18

17

14

17

12

17

BwtRleHuff

4

5

4

5

4

5

BwtMtfRleHuff

4

5

4

5

4

5

BwtRleAc fast

6

5

6

5

6

5

BwtMtfRleAc fast

4

5

4

5

4

5

BwtRleRc fast

6

5

6

5

6

5

BwtMtfRleRc fast

4

5

4

5

4

5

BwtRleRc med.

6

5

6

5

6

5

BwtMtfRleRc med.

4

5

4

5

4

5

BwtRleRc slow

6

5

6

5

6

5

BwtMtfRleRc slow

4

5

4

5

4

5

BwtWavelet

6

5

6

5

6

5

  1. Experimental results for the AA-15-DNA data set, with the UCD (left), NCD (middle), and CD (right) distance. For each compression algorithm, we report the partition distance for both UPGMA and NJ methods. Since the data set contains 15 species, the partition distance ranges from 0 to 50 in this case.